FORGOTTEN LINEAGES AND RECURRENT HYBRIDIZATIONS WITHIN THE KELP GENUS ALARIA (PHAEOPHYCEAE) REVEALED BY WHOLE GENOME SEQUENCING

Provided in this project are vcf files and occurrence data related to phylogenomic analysis of the kelp <i>Alaria</i>. All detailed methods, including filtering parameters, can be found in the article sharing this project title (article currently in review).<br>Alaria_occurence_data_2iv20.csv: occurrence data used for Fig. 1 map, sourced from records from Luning 1990 (Biogeography of Seaweeds), Barcode of Life Data Systems, and Macroalgal Portal.<br><br>Alaria_phylogenomics_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_final_LD.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, with additional filter for linkage disequilibrium, mapping reads to reference nuclear scaffolds (KU-791D_nuclear_scaffolds_fasta).<br><br>Alaria_phylogenomics_SNP_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to KU-791D_nuclear_scaffolds.fasta. This file has no SNP filters applied to it.<br><br>Alaria_Undaria_final_raw.vcf.gz: Raw vcf file after compiling bam files and calling SNPs, after read mapping of Alaria samples to Undaria pinnatifida genome (Shan et al. 2020). This file has no SNP filters applied to it.<br><br>Alaria_Undaria_SNP_final.fasta: Final SNP dataset in fasta format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>Alaria_Undaria_SNP_final.vcf.gz: Final SNP dataset in vcf format used for phylogenetic analysis of Alaria, including Undaria pinnatifida to act as an outgroup taxon, mapping reads to Undaria pinnatifida genome (Shan et al. 2020).<br><br>KU-791D_nuclear_scaffolds.fasta: reference nuclear scaffolds for Alaria esculenta used for mapping reads from various species of Alaria.<br>